Proteomic analyses are revolutionizing the diagnosis of human disease. Existing technologies are able to pinpoint the proteins indicative of disease progression, enabling their use in early detection and treatment scenarios. However, the use of proteomic techniques is limited because of the complexities of their usage and data interpretation. As an alternative to the current methods of peptide and protein analysis, I propose employing novel peptide-specific nucleic acid aptamers in the Proximity Ligation Assay for the detection of unique peptides in complex mixtures. In this system, a pair of aptamers would recognize the terminal ends of a peptide and, by virtue of their proximity, be enzymatically ligated together. Because most peptides are uniquely specified by their terminal sequences, the ligation product indicates a unique peptide. The presence of a peptide can be assessed via a PCR reaction, instead of its identification by mass. Using this novel method, one could quantitate peptide concentrations, identify low-abundance peptides and detect post-translation modifications, potentially in a single reaction. We envision adapting the method to readout via a microarray, simplifying complex protein mixture measurements to a single chip platform.